A method for detecting nuclear species in a sample by adaptive scanning using nuclear resonance fluorescence may comprise illuminating the target sample with photons from a source; detecting a signal in an energy channel; determining a scan evaluation parameter using the signal detected; determining whether the scan evaluation parameter meets a detection efficiency criterion; adjusting one or more system parameters such that the scan evaluation parameter meets the detection efficiency criterion; and comparing the signal in an energy channel to a predetermined species detection criterion to identify a species detection event. In another embodiment, detecting a signal in an energy channel may further comprise detecting photons scattered from the target sample. In another embodiment, detecting a signal in an energy channel may further comprise detecting photons transmitted through the target sample and scattered from at least one reference scatterer.