-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
Originator-Key-Asymmetric:
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 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 IuxjpWlWGvaaJi2G56O3Uxb3BHnENo0J/B1NjnVCRgfMuzi0NDMLHotRQTQM9gmt
 zFuK/RcpMa8HDI6xdFwGIw==

<SEC-DOCUMENT>0000914190-05-000430.txt : 20051107
<SEC-HEADER>0000914190-05-000430.hdr.sgml : 20051107
<ACCEPTANCE-DATETIME>20051107121351
ACCESSION NUMBER:		0000914190-05-000430
CONFORMED SUBMISSION TYPE:	3
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20051101
FILED AS OF DATE:		20051107
DATE AS OF CHANGE:		20051107

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Dalland Donald G
		CENTRAL INDEX KEY:			0001342907

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-01388
		FILM NUMBER:		051182612

	BUSINESS ADDRESS:	
		BUSINESS PHONE:		507-684-3721

	MAIL ADDRESS:	
		STREET 1:		906 FIFTH AVENUE EAST
		CITY:			ELLENDALE
		STATE:			MN
		ZIP:			56026

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>3
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2005-11-01</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001342907</rptOwnerCik>
            <rptOwnerName>Dalland Donald G</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>906 FIFTH AVENUE EAST</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>ELLENDALE</rptOwnerCity>
            <rptOwnerState>MN</rptOwnerState>
            <rptOwnerZipCode>56026</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>VP, Engineering and Operations</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>6824</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.833</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>1998-02-05</value>
            </exerciseDate>
            <expirationDate>
                <value>2008-02-05</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>4875</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.625</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>1999-02-05</value>
            </exerciseDate>
            <expirationDate>
                <value>2009-02-05</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>4875</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>4.00</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2000-02-05</value>
            </exerciseDate>
            <expirationDate>
                <value>2010-02-05</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>4875</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>8.384</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2010-10-27</value>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2015-10-27</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>30000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Subject to acceleration upon the Company reaching certain targets.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Donald G. Dalland</signatureName>
        <signatureDate>2005-11-04</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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