Abstract:Iranian ponds and water ecosystems are valuable assets which play decisive roles in economic, social, security and political affairs. Within the past few years, many Iranian water ecosystems such asUrmia Lake, Karoun River and Anzali Pond have been under disappearance threat. Ponds are habitats which cannot be replaced and this makes it necessary to investigate their changes in order to save these valuable ecosystems. The present research aims to investigate and evaluate the trend of variations in Anzali Pond using meteorological data between 1991-2010 by means of GMDH, which is based upon genetic algorithm and is a powerful technique in modeling complex dynamic non-linear systems, and linear regression technique. Input variables of both methodsinclude all factors (inside system and outside system factors) which affect variations in Anzali Pond. Exactness of linear regression method was 78% and exactness of GMDH neural network method was more than 97%. As as result, exactness of GMDH neural network method is significantly better than regression model.