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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 NxLD8BdGchsDnH2UWVqqTByTjKZultr0XdIqxbhjzdrD3dB6v+NVilCV2o0TpSc1
 Qf7Ec/GdUy+0nks2cWKmXQ==

<SEC-DOCUMENT>0000914190-05-000418.txt : 20051028
<SEC-HEADER>0000914190-05-000418.hdr.sgml : 20051028
<ACCEPTANCE-DATETIME>20051028145153
ACCESSION NUMBER:		0000914190-05-000418
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20051027
FILED AS OF DATE:		20051028
DATE AS OF CHANGE:		20051028

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			WATERS INSTRUMENTS INC
		CENTRAL INDEX KEY:			0000104987
		STANDARD INDUSTRIAL CLASSIFICATION:	POWER, DISTRIBUTION & SPECIALTY TRANSFORMERS [3612]
		IRS NUMBER:				410832194
		STATE OF INCORPORATION:			MN
		FISCAL YEAR END:			0630

	BUSINESS ADDRESS:	
		STREET 1:		2950 XENIUM LANE NORTH
		STREET 2:		SUITE 108
		CITY:			MINNEAPOLIS
		STATE:			MN
		ZIP:			55441
		BUSINESS PHONE:		5072887777

	MAIL ADDRESS:	
		STREET 1:		2411 7TH ST NW
		CITY:			ROCHESTER
		STATE:			NY
		ZIP:			56001

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	FLO TRONICS INC
		DATE OF NAME CHANGE:	19710602

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			COURTNEY EUGENE W
		CENTRAL INDEX KEY:			0001057095
		STANDARD INDUSTRIAL CLASSIFICATION:	SEMICONDUCTORS & RELATED DEVICES [3674]
		STATE OF INCORPORATION:			MN
		FISCAL YEAR END:			0831

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-01388
		FILM NUMBER:		051162878

	BUSINESS ADDRESS:	
		STREET 1:		7312 CLAREDON DR
		CITY:			EDINA
		STATE:			MN
		ZIP:			55439
		BUSINESS PHONE:		6124432500

	MAIL ADDRESS:	
		STREET 1:		P O BOX 5000
		STREET 2:		1495 STEIGER LAKE LANE
		CITY:			VICTORIA
		STATE:			MN
		ZIP:			55386
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2005-10-27</periodOfReport>

    <issuer>
        <issuerCik>0000104987</issuerCik>
        <issuerName>WATERS INSTRUMENTS INC</issuerName>
        <issuerTradingSymbol>WTRS</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001057095</rptOwnerCik>
            <rptOwnerName>COURTNEY EUGENE W</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>7312 CLAREDON DRIVE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>EDINA</rptOwnerCity>
            <rptOwnerState>MN</rptOwnerState>
            <rptOwnerZipCode>55439</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>4.52</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2003-10-21</value>
            </exerciseDate>
            <expirationDate>
                <value>2013-10-21</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>5025</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>5025</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>8.384</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2005-10-27</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>5000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2005-10-27</value>
            </exerciseDate>
            <expirationDate>
                <value>2015-10-27</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>5000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>5000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes></footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Eugene W. Courtney</signatureName>
        <signatureDate>2005-10-27</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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