Lakes are important components for regulating carbon cycling within landscapes. Most lakes are regarded as CO2 sources to the atmosphere, except for a few eutrophic ones. Algal blooms are common phenomena in many eutrophic lakes and can cause many environmental stresses, yet their effects on the net exchange of CO2 (FCO2) at large spatial scales have not been adequately addressed. We integrated remote sensing and Eddy Covariance (EC) technologies to investigate the effects that algal blooms have on FCO2 in the western basin of Lake Erie—a large lake infamous for these blooms. Three years of long-term EC data (2012–2014) at two sites were analyzed. We found that at both sites: (1) daily FCO2 significantly correlated with daily temperature, light, and wind speed during the algal bloom periods; (2) monthly FCO2 was negatively correlated with chlorophyll-a concentration; and (3) the year with larger algal blooms was always associated with lower carbon emissions. We concluded that large algal blooms could reduce carbon emissions in the western basin of Lake Erie. However, considering the complexity of processes within large lakes, the weak relationship we found, and the potential uncertainties that remain in our estimations of FCO2 and chlorophyll-a, we argue that additional data and analyses are needed to validate our conclusion and examine the underlying regulatory mechanisms.