Ammonium nitrogen and total germanium are among the main pollutants in the wastewater discharged from the leather industry. The intake of high concentrations of ammonium nitrogen and/or total germanium harms human health and biological species, as is well documented in literature. This paper focuses on assessing the trends of ammonium nitrogen and total germanium concentrations through time in two watersheds (Aojiang and Oujiang) in the Wenzhou metropolitan area of Zhejiang Province and their relationships with the released wastewater using regression and correlation statistics. The paper also utilizes the integrated pollution index to evaluate water quality in the two watersheds. Preliminary results show that, from 1992 to 1998 in the Aojing watershed, the concentrations of ammonium nitrogen and total germanium increased 13 and 14 times, respectively, decreasing somewhat after 1998, while between 1992 and 1997 in the Oujiang watershed, the concentrations increased, then decreased after 1997. The concentrations of ammonium nitrogen and total germanium are positively related to the amount of released wastewater. The concentrations of ammonium nitrogen and total germanium exceeded water standards 12 and 3 times, respectively, in Pingyang county of the Aojiang watershed, 14 and 3.3 times in Lucheng District of the Oujiang watershed, and 14 and 3.8 times in the Ouhai Oujiang watershed, respectively. In Pingyang county of the Aojiang watershed, the water quality degraded from Type III in 1992 to over Type V in 2003, and in the Oujiang watershed, the water quality degraded from Type II to over Type IV in 1999, when they were compared with the water quality standards. The water quality slightly improved in 2003 for the Oujiang watershed. It appears that pollution did have a direct positive correlation with leather industry production in the Pingyang Aojing watershed, while there was a negative correlation between the two in the Oujiang watershed. In these two watersheds, the integrated pollution index did not appear to relate to population dynamics and agricultural production. This paper also discusses the current new methodologies and approaches adopted nationally and internationally to reduce the contaminants and purify the environment for maintaining a sustainable and healthier environment in Wenzhou.