TheincreasingriverinepollutantshaveresultedinnutrientenrichmentanddeteriorationofwaterqualityinthecoastalwaterofGuangxiProvince,China.However,thequantitativerelationshipbetweennutrientloadsandwaterqualityresponses,whichiscrucialfordevelopingeutrophicationcontrolstrategies,isnotwellstudied.Inthisstudy,theriverinefluxesofnutrientswerequantifiedandintegratedwithnutrientcyclingandphytoplanktondynamicsbyusingboxmodelsforGuangxicoastalbays.Themodelconceptsandbiogeochemicalequationswerethesame;whilemostmodelparameterswerespecificforeachbay.Theparameterswerecalibratedwithseasonalobservationsduring2006–2007,andvalidatedwithyearlyaveragedmeasurementsin2009.Thegeneralfeaturesofnutrientandphytoplanktondynamicswerereproduced,andthemodelswereprovedfeasibleunderawiderangeofbayconditions.DissolvedinorganicnitrogenwasdepletedduringthespringalgalbloominZhenzhuBayandFangchengBaywithrelativelylessnutrientinputs.Phosphorusconcentrationwashighinspring,whichdecreasedthenduetocontinuousphytoplanktonconsumption.Chlorophyll-aconcentrationreacheditsannualmaximuminsummer,butwastheminimuminwinter.EutrophicationwascharacterizedbybothanincreaseinnutrientconcentrationsandphytoplanktonbiomassinLianzhouBay.Eitherabout80%reductionofnitrogenor70%reductionofphosphoruswasrequiredtocontrolthealgalbloominLianzhouBay.DefectsofthemodelswerediscussedandsuggestionstotheenvironmentalprotectionofGuangxicoastalbayswereproposed.