The debate about whether measurement reactivity exists in daily diary research on substance use is still unsettled due to the issues of study design and statistical methodology. This study proposes a time-varying effect model (TVEM) that characterizes the trajectory of substance use behaviors with nonparametric functions determined by the data rather than imposes presumed parametric functions. It also allows researchers to investigate the effect of measurement reactivity on not only the likelihood of using substances but also the amount of substance use. The TVEM was applied to analyze diary data on alcohol and marijuana use collected from an experiment, which randomized 307 participants in Michigan into daily and weekly assessment schedules during 2014-2016. This study found short-term measurement reactivity on alcohol use, but did not find a significant reactivity effect on marijuana use. The daily group had smaller odds of abstinence from drinking but lower expected drinking quantity in the first week of assessment, which dissipated by the second week. The results indicate that although daily self-monitoring could have short-term reactivity on substance use behaviors that tend to fluctuate across days, such as alcohol use, it does not affect substance use behaviors that are quite consistent, such as marijuana use. Our findings imply that although daily monitoring of drinking may motivate people to reduce the quantity consumed once they start to drink, it may also arouse their desire to start drinking. Yet, both effects tend to last only one week, as participants accommodate to the monitoring by the second week