Double-check to confirm that the flow was rising when you collected your samples. For example, if you sampled the water column and found low levels of phosphorus, you shouldn't necessarily conclude that there isn't a problem. There might be high levels of phosphorus in the bottom sediments, or in use by aquatic plants. To investigate this possibility, check your samplers' field notes to see if they recorded evidence of nutrient enrichment, such as algae blooms. For example, dissolved oxygen is typically lowest in the morning and highest in the late afternoon.
Professional scientists have the same problem.
Your data may be inconclusive, especially if you've only been monitoring for a single season. Don't go out on a limb if you're uncertain. It's perfectly valid to conclude that you need additional information in order to understand a system as complicated as a river. Maybe you need to conduct a shoreline survey or habitat assessment, or monitor additional indicators or sites. Make it a collaborative effort.