-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
Originator-Key-Asymmetric:
 MFgwCgYEVQgBAQICAf8DSgAwRwJAW2sNKK9AVtBzYZmr6aGjlWyK3XmZv3dTINen
 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 ErN9nGCz9qiRqppu2fgChQWTgUB1G0UBDFM+UQJKMa3zR5FGq8zXV+vXpzRzOwQP
 35Twedb5+uZBwiZ7e+IYUw==

<SEC-DOCUMENT>0000914190-05-000421.txt : 20051028
<SEC-HEADER>0000914190-05-000421.hdr.sgml : 20051028
<ACCEPTANCE-DATETIME>20051028145433
ACCESSION NUMBER:		0000914190-05-000421
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20051027
FILED AS OF DATE:		20051028
DATE AS OF CHANGE:		20051028

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			NORDQUIST DALE
		CENTRAL INDEX KEY:			0001057094
		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:		051162896

	BUSINESS ADDRESS:	
		BUSINESS PHONE:		6124432500

	MAIL ADDRESS:	
		STREET 1:		1495 STEIGER LAKE LANE
		CITY:			VICTORIA
		STATE:			MN
		ZIP:			55386

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
</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>0001057094</rptOwnerCik>
            <rptOwnerName>NORDQUIST DALE</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1950 EXCEL DRIVE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>MANKATO</rptOwnerCity>
            <rptOwnerState>MN</rptOwnerState>
            <rptOwnerZipCode>56001</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>8.47</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2004-11-04</value>
            </exerciseDate>
            <expirationDate>
                <value>2014-11-03</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>Common Stock (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/ Dale A. Nordquist</signatureName>
        <signatureDate>2005-10-27</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
-----END PRIVACY-ENHANCED MESSAGE-----