Hypothesis test for repeated water quality measurements?

#1
Hi, thanks for reading my post. I am working on my thesis project and not sure how to run a hypothesis test on some of the data. This part of the experiment involves measuring various water-quality parameters of fish effluent in response to two different fish feeds.

My 60-day experimental trial has two treatment levels, each with three replicates (currently on day 32). Every few days, I sample water from each of the 6 experimental units and measure pH, dissolved oxygen, nitrates, phosphates, etc. For each of these water-quality parameters (IVs), the time between sampling is not uniform. However, for each parameter, all replicates are sampled at the same time. For example, I may have taken samples for nitrates on days 1, 4, 6, 10, 12, 18, 22, etc. of the experiment, and on each of these days all replicates were sampled for nitrates.

The two treatment levels are two different types of fish feed. While the compositions of the two feeds do not change during the trial, the quantities fed to each replicate change (mostly increase) over the course of the trial. The amount of feed given to the fish in a given replicate on a given day is calculated based on (1) an estimate of the weight of the fish in that replicate on that day and (2) a feeding rate.

To help me visualize the data as the trial progresses, I input each parameter's data points in Excel and create graphs with the parameter on the y-axis and the day# on the x-axis. Thus, each graph shows the trajectories of one parameter for each of the 6 replicates over time. I need a hypothesis test to, for example, test whether the nitrate levels are different between treatments. I do not expect much interaction between the various IVs. I have tried running repeated measures ANOVA in SPSS, but this test does not seem to fit the experimental design.

Any advice?