Nitrogen measurement in estuaries is complicated by salinity effects on the normal spectrophometric methods used for the determination of nitrate, ammonia, urea etc. The wide range of concentrations found in estuaries due to freshwater inputs and tidal effects is also problematic. Newer in situ instrumentation is improving but the contribution from ammonia and nitrate to total N is variable, So I am not sure that a neasy "one size fits all method exists but certainly robust salinity measurement s essential.
Systematic salt effects in the automated determination of nutrients in seawater B.M.Stewart and P.A.W.Elliott Water Research Volume 30, Issue 4, April 1996, Pages 869-874