You can apply statistical tools such as SPSS and MS Excel.  Correlation  analysis, regression, ANOVA, cluster and factor analyses will aid to shed immense light on the relationship when applied with dexterity. You are likely to be amazed at the depth of information that will be unfolded.

What is the best method is a complicated question, but GLM is a valid one. Also, have a look at GAM which works roughly the same way but might give you a slightly better fit. . 

SPSS can be used to identify impact and variation of  zooplankton and fish growth rate. It also very good in identifying the socio-economic impacts. The accuracy will be good based on the sample size...

Dear Imoukhuede, Nils and Konstantin

Thanks a lot for your help.

Heiarchial cluster analysis, component analysis can be done to study the direct and the indirect interaction and interrealtion between the zooplankton community and the fish growth rate.... SPSS and SYSTAT can be used for the same...

Dear Sheju Thomas

Thanks a lot for your comment