A direct method to verify uncertainties in inventory systems for biogenic hydrocarbons entails the comparison between flux measurements and model outputs derived at the landscape level. This approach is not only prohibitively expensive and logistically unfeasible, but also only possible for selected sites and brief periods of the season. As a result, monitoring agencies prefer to make ambient concentration measurements on a routine basis as a means to represent the source strength for the given domain. Ambient hydrocarbon concentration data can be used to deduce the source strength of the surrounding landscape provided that local sources and sinks can be properly characterized. Owing to the heterogeneous nature of hydrocarbon sources, regulatory modeling systems reportedly include uncertainties reaching sevenfold compared to source strength measurements. At present it is not known whether errors in emission models are due to theoretical limitations or the specification of source distribution within the region of interest. Our goal here is to address this issue by developing and testing a modeling system to infer the source strength of biogenic hydrocarbons for forested ecosystems. Using ambient hydrocarbon concentrations we estimate emissions by employing a one-dimensional model that accounts for the chemical sinks and the vertical turbulent exchange of hydrocarbons. For the latter we formulate an algorithm to describe the diurnal variation of the mixed boundary layer depth where gases remain confined during the daytime whereas for the former we employ chemical mechanisms of recent vintage to characterize the hydrocarbon sinks in the system. To verify its usefulness, we apply the model to two contrasting forested ecosystems. Situated in the boreal biome of Canada away from anthropogenic influences, one forest consists of a stand with uniform and well-characterized hydrocarbon sources. The second temperate forest comprises mixed deciduous trees whose hydrocarbon emissions vary greatly among species, and is frequently impacted by anthropogenic sources.