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Containment basins (CB) are an integral part of recycling irrigation systems that foster agricultural sustainability through water resource conservation. However, little is known regarding this aquatic ecosystem and the lack of water quality data has become an increasingly serious liability in crop health management. Here we report on four distinct seasonal and two diurnal patterns of change in water quality in the CBs. The four seasonal patterns are (a) periodic fluctuation in chlorophyll a, pH, and dissolved oxygen (DO), (b) oxidation-reduction potential (ORP) rises with decreasing DO, (c) tendency for increase in electrical conductivity, salinity, and total dissolved solids, and (d) weather-dependent changes in turbidity and temperature. The two diurnal patterns are (1) chlorophyll a, pH, DO, and temperature consistently peak between 16:00 and 17:00 hours and bottom out around 08:00 hours, and (2) ORP peaks in the morning and bottoms in the evening. Eight of the nine parameters excluding temperature were correlated; and algal blooms appear to be a major driving force for changes in the other seven parameters. These results underscore the importance of water quality monitoring in irrigation management and provide a framework for better understanding of pathogen aquatic ecology and how changes in water quality might be employed in a manner that suppresses plant pathogens and improves crop quality and productivity.