<?xml version="1.0" encoding="us-ascii"?><InstanceReport xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema"><Version>2.2.0.25</Version><hasSegments>false</hasSegments><hasScenarios>false</hasScenarios><ReportLongName>0201 - Disclosure - Organization and Basis of Presentation</ReportLongName><DisplayLabelColumn>true</DisplayLabelColumn><ShowElementNames>false</ShowElementNames><RoundingOption /><HasEmbeddedReports>false</HasEmbeddedReports><Columns><Column><Id>1</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelColumn>false</LabelColumn><CurrencyCode>USD</CurrencyCode><FootnoteIndexer /><hasSegments>false</hasSegments><hasScenarios>false</hasScenarios><MCU><KeyName>1/1/2011 - 3/31/2011
USD ($)

USD ($) / shares

</KeyName><CurrencySymbol>$</CurrencySymbol><contextRef><ContextID>Jan-01-2011_Mar-31-2011</ContextID><EntitySchema>http://www.sec.gov/CIK</EntitySchema><EntityValue>0000225648</EntityValue><PeriodDisplayName /><PeriodType>duration</PeriodType><PeriodStartDate>2011-01-01T00:00:00</PeriodStartDate><PeriodEndDate>2011-03-31T00:00:00</PeriodEndDate><Segments /><Scenarios /></contextRef><UPS><UnitProperty><UnitID>USD</UnitID><UnitType>Standard</UnitType><StandardMeasure><MeasureSchema>http://www.xbrl.org/2003/iso4217</MeasureSchema><MeasureValue>USD</MeasureValue><MeasureNamespace>iso4217</MeasureNamespace></StandardMeasure><Scale>0</Scale></UnitProperty><UnitProperty><UnitID>USDEPS</UnitID><UnitType>Divide</UnitType><NumeratorMeasure><MeasureSchema>http://www.xbrl.org/2003/iso4217</MeasureSchema><MeasureValue>USD</MeasureValue><MeasureNamespace>iso4217</MeasureNamespace></NumeratorMeasure><DenominatorMeasure><MeasureSchema>http://www.xbrl.org/2003/instance</MeasureSchema><MeasureValue>shares</MeasureValue><MeasureNamespace>xbrli</MeasureNamespace></DenominatorMeasure><Scale>0</Scale></UnitProperty><UnitProperty><UnitID>Shares</UnitID><UnitType>Standard</UnitType><StandardMeasure><MeasureSchema>http://www.xbrl.org/2003/instance</MeasureSchema><MeasureValue>shares</MeasureValue><MeasureNamespace>xbrli</MeasureNamespace></StandardMeasure><Scale>0</Scale></UnitProperty></UPS><CurrencyCode>USD</CurrencyCode><OriginalCurrencyCode>USD</OriginalCurrencyCode></MCU><CurrencySymbol>$</CurrencySymbol><Labels><Label Id="1" Label="3 Months Ended" /><Label Id="2" Label="Mar. 31, 2011" /></Labels></Column></Columns><Rows><Row><Id>2</Id><IsAbstractGroupTitle>true</IsAbstractGroupTitle><Level>0</Level><ElementName>us-gaap_GeneralPoliciesAbstract</ElementName><ElementPrefix>us-gaap</ElementPrefix><IsBaseElement>true</IsBaseElement><BalanceType>na</BalanceType><PeriodType>duration</PeriodType><ShortDefinition>No definition available.</ShortDefinition><IsReportTitle>false</IsReportTitle><IsSegmentTitle>false</IsSegmentTitle><IsSubReportEnd>false</IsSubReportEnd><IsCalendarTitle>false</IsCalendarTitle><IsTuple>false</IsTuple><IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow><IsEquityAdjustmentRow>false</IsEquityAdjustmentRow><IsBeginningBalance>false</IsBeginningBalance><IsEndingBalance>false</IsEndingBalance><IsReverseSign>false</IsReverseSign><PreferredLabelRole /><FootnoteIndexer /><Cells><Cell><Id>1</Id><IsNumeric>false</IsNumeric><IsRatio>false</IsRatio><DisplayZeroAsNone>false</DisplayZeroAsNone><NumericAmount>0</NumericAmount><RoundedNumericAmount>0</RoundedNumericAmount><NonNumbericText /><NonNumericTextHeader /><FootnoteIndexer /><CurrencyCode /><CurrencySymbol /><IsIndependantCurrency>false</IsIndependantCurrency><ShowCurrencySymbol>false</ShowCurrencySymbol><DisplayDateInUSFormat>false</DisplayDateInUSFormat><hasSegments>false</hasSegments><hasScenarios>false</hasScenarios></Cell></Cells><OriginalInstanceReportColumns /><Unit>Other</Unit><ElementDataType>xbrli:stringItemType</ElementDataType><SimpleDataType>string</SimpleDataType><ElementDefenition>No definition available.</ElementDefenition><IsTotalLabel>false</IsTotalLabel><IsEPS>false</IsEPS><Label>Organization and Basis of Presentation [Abstract]</Label></Row><Row><Id>3</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><Level>0</Level><ElementName>us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock</ElementName><ElementPrefix>us-gaap</ElementPrefix><IsBaseElement>true</IsBaseElement><BalanceType>na</BalanceType><PeriodType>duration</PeriodType><ShortDefinition>No definition available.</ShortDefinition><IsReportTitle>false</IsReportTitle><IsSegmentTitle>false</IsSegmentTitle><IsSubReportEnd>false</IsSubReportEnd><IsCalendarTitle>false</IsCalendarTitle><IsTuple>false</IsTuple><IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow><IsEquityAdjustmentRow>false</IsEquityAdjustmentRow><IsBeginningBalance>false</IsBeginningBalance><IsEndingBalance>false</IsEndingBalance><IsReverseSign>false</IsReverseSign><PreferredLabelRole>verboselabel</PreferredLabelRole><FootnoteIndexer /><Cells><Cell><Id>1</Id><IsNumeric>false</IsNumeric><IsRatio>false</IsRatio><DisplayZeroAsNone>false</DisplayZeroAsNone><NumericAmount>0</NumericAmount><RoundedNumericAmount>0</RoundedNumericAmount><NonNumbericText>&lt;!--DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd" --&gt;
   &lt;!-- Begin Block Tagged Note 1 - us-gaap:OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock--&gt;
   &lt;div align="left" style="margin-left: 0%"&gt;&lt;!-- XBRL,ns --&gt;
   &lt;!-- xbrl,nx --&gt;
   &lt;div align="center" style="margin-left: 0%; margin-right: 0%; font-size: 10pt; font-family: Arial, Helvetica; color: #000000; background: transparent"&gt;
   &lt;b&gt;&lt;font style="font-family: 'Times New Roman', Times"&gt;
   &lt;/font&gt;&lt;/b&gt;
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; font-size: 10pt; font-family: Arial, Helvetica; color: #000000; background: transparent"&gt;
       &lt;b&gt;&lt;font style="font-family: 'Times New Roman', Times"&gt;NOTE&amp;#160;1.
       ORGANIZATION AND BASIS OF PRESENTATION&lt;/font&gt;&lt;/b&gt;
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; text-indent: 1%; font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent"&gt;
       The terms &amp;#8220;we,&amp;#8221; &amp;#8220;our,&amp;#8221; &amp;#8220;ours,&amp;#8221;
       &amp;#8220;us&amp;#8221; and &amp;#8220;Company&amp;#8221; refer to Covanta Holding
       Corporation and its subsidiaries; the term &amp;#8220;Covanta
       Energy&amp;#8221; refers to our subsidiary Covanta Energy Corporation
       and its subsidiaries.
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; font-size: 10pt; font-family: Arial, Helvetica; color: #000000; background: transparent"&gt;
       &lt;b&gt;&lt;font style="font-family: 'Times New Roman', Times"&gt;Organization&lt;/font&gt;&lt;/b&gt;
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; text-indent: 1%; font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent"&gt;
       We are one of the world&amp;#8217;s largest owners and operators of
       infrastructure for the conversion of waste to energy (known as
       &amp;#8220;energy-from-waste&amp;#8221; or &amp;#8220;EfW&amp;#8221;), as well as
       other waste disposal and renewable energy production businesses.
       Energy-from-waste serves two key markets as both a sustainable
       waste disposal solution that is environmentally superior to
       landfilling and as a source of clean energy that reduces overall
       greenhouse gas emissions and is considered renewable under the
       laws of many states and under federal law. Our facilities are
       critical infrastructure assets that allow our customers, which
       are principally municipal entities, to provide an essential
       public service.
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; text-indent: 1%; font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent"&gt;
       We operate
       &lt;font style="white-space: nowrap"&gt;and/or&lt;/font&gt; have
       ownership positions in 44 energy-from-waste facilities, which
       are primarily located in North America, and 18 additional energy
       generation facilities, including other renewable energy
       production facilities in North America (wood biomass, landfill
       gas and hydroelectric) and independent power production
       (&amp;#8220;IPP&amp;#8221;) facilities in Asia. We hold equity interests
       in energy-from-waste facilities in China and Italy. We also
       operate waste management infrastructure that is complementary to
       our core EfW business.
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; text-indent: 1%; font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent"&gt;
       We have one reportable segment which is Americas and is
       comprised of waste and energy services operations primarily in
       the United States and Canada. For additional information, see
       Note&amp;#160;6. Financial Information by Business Segments.
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; text-indent: 1%; font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent"&gt;
       In 2010, we adopted a plan to sell our interests in our fossil
       fuel independent power production facilities in the Philippines,
       India, and Bangladesh. During the first quarter of 2011, we
       completed the sale of our interests in a 510 megawatt
       (&amp;#8220;MW&amp;#8221;) (gross) coal-fired electric power generation
       facility in the Philippines (&amp;#8220;Quezon&amp;#8221;) and we
       completed the sale of our majority equity interests in a
       106&amp;#160;MW (gross) heavy fuel-oil fired electric power
       generation facilities in Tamil Nadu, India
       (&amp;#8220;Samalpatti&amp;#8221;). In April 2011, we signed an agreement
       to sell our majority equity interests in our 106&amp;#160;MW (gross)
       heavy fuel-oil fired electric power generation facility also in
       Tamil Nadu, India (&amp;#8220;Madurai&amp;#8221;). The remaining asset
       held for sale is our equity interest in a barge-mounted
       126&amp;#160;MW (gross) diesel/natural gas-fired electric power
       generation facility located near Haripur, Bangladesh. See
       Note&amp;#160;4. Assets Held for Sale and Dispositions and
       Note&amp;#160;15. Subsequent Event for additional information.
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; font-size: 10pt; font-family: Arial, Helvetica; color: #000000; background: transparent"&gt;
       &lt;b&gt;&lt;font style="font-family: 'Times New Roman', Times"&gt;Basis of
       Presentation&lt;/font&gt;&lt;/b&gt;
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; text-indent: 1%; font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent"&gt;
       The accompanying unaudited condensed consolidated financial
       statements have been prepared in accordance with United States
       generally accepted accounting principles (&amp;#8220;GAAP&amp;#8221;) and
       with the instructions to
       &lt;font style="white-space: nowrap"&gt;Form&amp;#160;10-Q&lt;/font&gt;
       and Article&amp;#160;10 of
       &lt;font style="white-space: nowrap"&gt;Regulation&amp;#160;S-X.&lt;/font&gt;
       Accordingly, they do not include all information and footnotes
       required by GAAP for complete financial statements. In the
       opinion of management, all adjustments (including normal
       recurring accruals) considered necessary for fair presentation
       have been included in our financial statements. All intra-entity
       accounts and transactions have been eliminated. Operating
       results for the interim period are not necessarily indicative of
       the results that may be expected for the fiscal year ended
       December&amp;#160;31, 2011. This
       &lt;font style="white-space: nowrap"&gt;Form&amp;#160;10-Q&lt;/font&gt;
       should be read in conjunction with the Audited Consolidated
       Financial Statements and accompanying Notes in our Annual Report
       on
       &lt;font style="white-space: nowrap"&gt;Form&amp;#160;10-K&lt;/font&gt;
       for the year ended December&amp;#160;31, 2010
       &lt;font style="white-space: nowrap"&gt;(&amp;#8220;Form&amp;#160;10-K&amp;#8221;).&lt;/font&gt;
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; text-indent: 1%; font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent"&gt;
       We use the equity method to account for our investments for
       which we have the ability to exercise significant influence over
       the operating and financial policies of the investee.
       Consolidated net income includes our proportionate share of the
       net income or loss of these companies. Such amounts are
       classified as &amp;#8220;equity in net income from unconsolidated
       investments&amp;#8221; in our condensed consolidated financial
       statements. Investments in companies in which we do not have the
       ability to exercise significant influence are carried at the
       lower of cost or estimated realizable value. We monitor
       investments for
       &lt;font style="white-space: nowrap"&gt;other-than-temporary&lt;/font&gt;
       declines in value and make reductions when appropriate.
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; font-size: 10pt; font-family: Arial, Helvetica; color: #000000; background: transparent"&gt;
       &lt;b&gt;&lt;font style="font-family: 'Times New Roman', Times"&gt;Reclassifications&lt;/font&gt;&lt;/b&gt;
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; text-indent: 1%; font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent"&gt;
       As more fully described in Note&amp;#160;4. Assets Held for Sale and
       Dispositions, during the fourth quarter of 2010, the operations
       of our fossil fuel independent power production facilities held
       for sale met the criteria to be classified as
   discontinued operations. The assets and liabilities associated
       with these businesses are presented in our condensed
       consolidated balance sheets as &amp;#8220;Current Assets Held for
       Sale&amp;#8221; and &amp;#8220;Current Liabilities Held for Sale&amp;#8221;.
       The results of operations of these businesses are included in
       the condensed consolidated statements of operations as
       &amp;#8220;Income from discontinued operations, net of tax.&amp;#8221; The
       cash flows of these businesses are also presented separately in
       our condensed consolidated statements of cash flows. All
       corresponding prior year periods presented in our condensed
       consolidated financial statements and accompanying notes have
       been reclassified to reflect the discontinued operations
       presentation.
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; text-indent: 1%; font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent"&gt;
       During the first quarter of 2011, we corrected our presentation
       of the condensed consolidated balance sheet at December&amp;#160;31,
       2010 to adjust a portion of the excess of purchase price over
       par value for treasury stock transactions from additional
       paid-in capital to retained earnings. We have adjusted
       approximately $66&amp;#160;million to retained earnings from
       additional paid-in capital as of December&amp;#160;31, 2010. This
       change had no impact on total equity.
   &lt;/div&gt;
   &lt;/div&gt;
</NonNumbericText><NonNumericTextHeader>&lt;!--DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd" --&gt;
   &lt;!-- Begin Block Tagged Note</NonNumericTextHeader><FootnoteIndexer /><CurrencyCode /><CurrencySymbol /><IsIndependantCurrency>false</IsIndependantCurrency><ShowCurrencySymbol>false</ShowCurrencySymbol><DisplayDateInUSFormat>false</DisplayDateInUSFormat><hasSegments>false</hasSegments><hasScenarios>false</hasScenarios></Cell></Cells><OriginalInstanceReportColumns /><Unit>Other</Unit><ElementDataType>us-types:textBlockItemType</ElementDataType><SimpleDataType>string</SimpleDataType><ElementDefenition>Description containing the entire organization, consolidation and basis of presentation of financial statements disclosure. May be provided in more than one note to the financial statements, as long as users are provided with an understanding of (1) the significant judgments and assumptions made by an enterprise in determining whether it must consolidate a VIE and/or disclose information about its involvement with a VIE, (2) the nature of restrictions on a consolidated VIE's assets reported by an enterprise in its statement of financial position, including the carrying amounts of such assets, (3) the nature of, and changes in, the risks associated with an enterprise's involvement with the VIE, and (4) how an enterprise's involvement with the VIE affects the enterprise's financial position, financial performance, and cash flows.  Describes procedure if disclosures are provided in more than one note to the financial statements.</ElementDefenition><ElementReferences>Reference 1: http://www.xbrl.org/2003/role/presentationRef
 -Publisher FASB
 -Name FASB Staff Position (FSP)
 -Number FAS140-4 and FIN46(R)-8
 -Paragraph 8, C1, C7

Reference 2: http://www.xbrl.org/2003/role/presentationRef
 -Publisher AICPA
 -Name Accounting Research Bulletin (ARB)
 -Number 51
 -Paragraph 2-6

Reference 3: http://www.xbrl.org/2003/role/presentationRef
 -Publisher AICPA
 -Name Statement of Position (SOP)
 -Number 94-6
 -Paragraph 10

Reference 4: http://www.xbrl.org/2003/role/presentationRef
 -Publisher FASB
 -Name FASB Interpretation (FIN)
 -Number 46R
 -Paragraph 4, 14, 15

</ElementReferences><IsTotalLabel>false</IsTotalLabel><IsEPS>false</IsEPS><Label>Organization and Basis of Presentation</Label></Row></Rows><Footnotes /><NumberOfCols>1</NumberOfCols><NumberOfRows>2</NumberOfRows><ReportName>Organization and Basis of Presentation</ReportName><MonetaryRoundingLevel>UnKnown</MonetaryRoundingLevel><SharesRoundingLevel>UnKnown</SharesRoundingLevel><PerShareRoundingLevel>UnKnown</PerShareRoundingLevel><ExchangeRateRoundingLevel>UnKnown</ExchangeRateRoundingLevel><HasCustomUnits>false</HasCustomUnits><SharesShouldBeRounded>true</SharesShouldBeRounded></InstanceReport>
