Previous research has focused on dissolved organic carbon (DOC) as a surrogate for dissolved organic matter (DOM) in pharmaceutical wastewater. Dissolved organic nitrogen (DON) as a part of DOM has received little attention. This study investigated the removal characteristics of DON and its influence on the N-nitrosodimethylamine formation potential (NDMA FP) and acute toxicity of DOM in a full-scale hydrolysis/acidification + anaerobic/anoxic/aerobic + moving bed biofilm reactor (MBBR) process treating pharmaceutical wastewater. Results showed that maximum removal of DON (68 ± 12%) was present in the anaerobic process. The removal of DON by anoxic and aerobic processes was negligible as a result of the production of new N-containing compounds that are characteristic of proteins/amino sugars and lipids. DON concentration decreased significantly in the MBBR process (p < 0.05, t-test), indicating that manipulation of the solids retention times (SRTs) could be a solution to minimize DON. Based on the Pearson correlation analysis, the behavior of NDMA FP and DOM acute toxicity was significantly associated with the 3 kDa < MW < 10 kDa (r = 0.709, p < 0.05) and MW < 3 kDa DON (r = 0.659, p < 0.05), respectively, and are not identical to that of DOC fractions (r = 0.037-0.466, p = 0.051-0.886). Moreover, the removal and molecular changes of DON are not coupled with that of DOC during biotreatment. Thus, testing the performance indicator of DON in pharmaceutical wastewater was recommended, as it provides important information for DOM removal characteristics.