Are freshwater systems (eg flowing water, mesotrophic and eutrophic waters) sensitive to acid and nitrogen deposition?

Freshwater habitats have a complex interaction with air pollution and as such, APIS often states to seek site specific advice. This is because some freshwater habitat types may be sensitive to air pollution. You should use the relevant general freshwater type and pollutant combination for your assessment. For acidification there are pages on rivers  - and standing water/canals.
The APIS Habitat/Pollutant impacts tab can help for understanding the evidence for effects from air pollution types on different freshwater systems as well as other habitats. For example, the standing water and canals page for nitrogen deposition describes the nuances of nitrogen:phosphorus relationships and why it is difficult to then establish a critical load for all situations:

"A critical load cannot be given for nitrogen, as quantitative relationships between biology and nitrogen concentrations are poorly understood. The nitrogen to phosphorus ratio can be important, with a molar ratio of around 16:1 (7:1 by weight) being the threshold between N- and P-limitation (Wetzel 2001). Impacts could be assessed by deviation from a 'natural' ratio for an individual site."

If in doubt, seek site specific advice from the relevant authority (eg conservation agency or site manager).