Mitigating stream and river impairment is complex, particularly in mixed-land-use watersheds given the likelihood of integrated responses of stream restoration to coupled and ongoing terrestrial ecosystem disturbance and the need for periodic reassessment and maintenance. Traditional biological sampling (e.g., macroinvertebrate sampling or other biological indices) alone seldom identifies the cause of biological community impairment and large fiscal investments are often made with no apparent improvement to aquatic ecosystem health. A stream physical habitat assessment (PHA) can yield information that, when paired with land-use data may reveal causal patterns in aquatic physical habitat degradation and help to identify sites for rehabilitation or restoration. A rapid and customizable physical habitat assessment method (rPHA) is presented that reduces commonly high PHA time and labor costs while facilitating informative value. Sampling time is reduced to approximately 30–40 min per survey site with a crew of three individuals. The method is flexible and thus adaptable to varied applications and needs. The rPHA design facilitates replication at regular spatial and temporal intervals thereby informing land-use managers and agencies of current conditions and trends in habitat response to natural and anthropogenic stressors. The rPHA outcomes can thus provide science-based supplemental information to better inform management practices and stream restoration decisions in contemporary mixed-land-use watersheds.