Resurgences in toxic cyanobacterial blooms, especially Microcystis, have been observed in the lower Great Lakes over the last decade in areas where total phosphorus (TP) levels are below historically high levels. Compliance with regulatory standards for TP in municipal wastewater effluent has likely depended on increased use of iron chloride as a flocculating agent for phosphorus removal in some wastewater treatment plants (WWTP). Since some ecological research suggests that increased supply of biologically available forms of iron may stimulate cyanobacterial growth, TP and iron loadings from WWTPs in the Hamilton Harbour and Toronto areas were examined. TP loadings from the Hamilton and Toronto WWTPs over the last 10–15 years have, in general, not increased. Effluent sampling frequency for iron is much lower than for a regulated parameter such as TP, consequently there is greater uncertainty in loading estimates. Moreover, iron loading estimates are available for only one plant from 1996 and three plants from 1999 so long-term loading trends cannot be established. Iron loading from the Humber WWTP in Toronto increased 5-fold between 2001–2004 while iron loading from the Woodward WWTP in Hamilton is quite high for its size. Iron consumption (i.e., dosing) data are available for three plants from the early 1990s. There was a clear increase in iron consumption by the Burlington-Skyway WWTP beginning in 1997 which was accompanied by a clear decrease in TP loading. However, there were no clear long-term trends in iron consumption in the Toronto plants even when normalized for flow. Increased monitoring and reporting of iron in WWTP effluent by all WWTP operators is recommended along with a review of methods for iron retention.