The study of freshwater ecosystems is also known as limnology. Compared to terrestrial studies, limnic systems can be better delineated as their shorelines present clear boundaries between fundamentally different environments. Freshwater systems can be distinguished into lotic or flowing water and lentic or standing water systems. River habitats can be characterized by flow velocity and discharge, streambed, bank and riparian conditions, and habitat quality for organisms. Detailed instructions for appropriate measurements and collection methods for macrobenthos and fish are provided. We present simple quality indices for habitat, water quality, and macrobenthos that can be compared to other rivers. Detailed descriptions and instructions for studying lakes, including the vertical stratification of light, temperature, and dissolved oxygen (DO), are also provided. Methods for plankton sampling and calculating density estimates and biodiversity indices are presented. In addition, we describe how macrophytes at the shoreline of lakes can be surveyed and how these data can be presented in a density map. Waters that only carry water intermittently throughout the year are classified as temporary. These include small bodies of water known as temporary ponds with their specific fauna.