Despite warnings that clean fresh water is becoming increasingly scarce throughout the World, freshwater ecosystems continue to be under threat from economic development. The threat is worse in countries trying to build their economies and ⁄ or lack resources to protect their environment. Many economists have warned that economic development that destroys environmental resources is unsustainable. Local expertise needed to evaluate the water quality of lakes and flowing water systems is often missing. Many countries need capacity building programmes to help train young scientists in techniques commonly used to biomonitor aquatic ecosystems in the USA, Europe, Japan and South Korea. Biomonitoring of major groups of organisms can be less costly, relative to sophisticated instrumentation. Further, the presence of even tolerant biological organisms is more dependable than chemical concentrations that can vary continuously. The most effective groups of organisms for biomonitoring include the diatoms, which are often the dominant forms of algae in both lakes and riverine systems, aquatic insects, particularly mayflies, stoneflies and caddisflies, often referred to as the EPT and fishes. Biological methods can be used with an active adaptive management approach that provides guidance for remediation of polluted water systems by studying the levels of degradation or of recovery of ecosystems to or from a more normal state. This approach only can be effective as long the skills exist to understand ecosystems and properly identify lake and river flora and fauna.