Yes, you can decided to study the trends of specific water parameters from upstream to downstream. In addition, you can study trends during dry and wet seasons.
performed a study on "a review of currently available on-stream
water quality models and their applicability for simulating dissolved oxygen in lowland rivers". Major models used nowadays for describing water quality in freshwater systems, highlighted in this paper. SIMCAT, QUAL2E, TOMCAT, QUASAR, ISIS, MIKE-11, and each of their capabilities were discussed, concerning the issue of simulating dissolved oxygen in rivers located in lowlands. This review revealed that no particular model could provide satisfactory results. The author also discovered that all the models had limitations. He found that setting one model against another in relation to broad use, is not the best option, but rather a model of intermediate complexity like QUASAR was a better option in simulating DO in river systems.
Always. Pretty much any dataset can be subjected to a trend analysis. Basic requirement is good and logical knowledge of the uncertainties involved to be able to adequately assess the significance of the signals.