We present the Water Ecosystems Tool (WET) - a new generation of open-source, highly customizable aquatic ecosystem model. WET is a completely modularized aquatic ecosystem model developed in the syntax of the Framework for Aquatic Biogeochemical Models (FABM), which enables coupling to multiple physical models ranging from zero to three dimensions, and is based on the FABM-PCLake model. The WET model has been extensively modularized, empowering users with flexibility of food web configurations, and incorporates model features from other state-of-the-art models, with new options for nitrogen fixation and vertical migration. With the new structure, features and flexible customization options, WET is suitable in a wide range of aquatic ecosystem applications. We demonstrate these new features and their impacts on model behavior for a temperate lake for which a model calibration of the FABM-PCLake model was previously published and discuss the benefits of the new model.