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Freshwater Harmful Algal Blooms happen most often where there are high levels of nutrients like nitrogen or phosphorus present in warm, still waters like lakes, ponds, or reservoirs. They can also occur in rivers, especially during summer months. Aquatic ecosystems need nutrients to thrive but fertilizer runoff from agriculture, sewage and industrial discharges, and urban stormwater have added an excessive of nutrients into many of our nation’s bays, lakes and rivers.