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Fast radio burst (FRB) source 20180916B exhibits a 16.33-day periodicity in its burst activity. It is as of yet unclear what proposed mechanism produces the activity, but polarization information is a key diagnostic. Here, we report on the polarization properties of 44 bursts from FRB 20180916B detected between 2018 December and 2021 December by CHIME/FRB, the FRB project on the Canadian Hydrogen Intensity Mapping Experiment the Canadian Hydrogen Intensity Mapping Experiment. In contrast to previous observations, we find significant variations in the Faraday rotation measure (RM) of FRB 20180916B. Over the nine month period 2021 April$-$2021 December we observe an apparent secular increase in $\rm{RM}$ of $\sim 50 \; \rm{rad\, m^{-2}}$ (a fractional change of over $40\%$) that is accompanied by a possible drift of the emitting band to lower frequencies. This interval displays very little variation in the dispersion measure ($Δ\rm{DM}\lesssim 0.8\; \rm{pc\, cm^{-3}}$) which indicates that the observed RM evolution is likely produced from coherent changes in the Faraday-active medium's magnetic field. Burst-to-burst RM variations appear unrelated to the activity cycle phase. The degree of linear polarization of our burst sample ($\gtrsim 80\%$) is consistent with the negligible depolarization expected for this source in the 400-800 MHz bandpass of CHIME. FRB 20180916B joins other repeating FRBs in displaying substantial RM variations between bursts. This is consistent with the notion that repeater progenitors may be associated with young stellar populations by their preferential occupation of dynamic magnetized environments commonly found in supernova remnants, pulsar wind nebulae or near high mass stellar companions.