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An assessment framework for Tampa Bay Water's Hydrobiological Monitoring Program (HBMP) has been established based on the relationship between freshwater flow and primary environmental indicators monitored under the HBMP. The underlying paradigm is based on the understanding that reduced flows can result in water quality conditions adverse to biological populations if these conditions exceed a specific magnitude and/or are beyond a certain duration. HBMP water quality parameters identified as primary indicators include salinity (due to osmotic pressure controlling distribution of fish, benthos, and vegetation among other ecological effects), dissolved oxygen (due to the aerobic stress to fish and benthos that can occur due to depressed dissolved oxygen concentrations), and chlorophyll-a (due to excessive phytoplankton blooms that may increase biological oxygen demand and can result in depressed dissolved oxygen concentrations). These primary indicators were identified because they specifically relate to linkages in the HBMP conceptual model as well as State of Florida water quality standards and a great deal of effort has been allocated to understanding these relationships. To this end, special studies have been implemented to further scientific information related to the effects of flows and withdrawals on the magnitude, duration, and distribution of phytoplankton as one aspect of the larger HBMP assessment framework. In this paper, we provide a summary of recent special studies completed in the lower Alafia River, focused on in situ fluorometer chlorophyll-a measurement, interpretation, and predictive capability. We share lessons learned and our steps for moving forward in efforts to relate flow (and withdrawal-related effects) on phytoplankton in the lower Alafia River. [ABSTRACT FROM AUTHOR]