In this paper, we investigated the impact on dwell time of station design, train load, and passenger flow, considering boarding fraction. We employed system-wide automated data sources including automatic passenger counting and automatic vehicle location data in the rail transit system in Calgary, Canada. Regression analyses were conducted to achieve accurate dwell time estimation by calculating passenger load per car, boarding, and alighting passengers per door, and also identifying the critical door with the highest demand. Observations for each critical door were divided based on the fraction of boarding passengers with respect to the sum of boarding and alighting. Six stations with distinct geometric designs were selected for comparison to assess their impact on dwell time. The results indicate that, for dominant boarding or alighting, a longer time is needed per passenger to alight or board, respectively. Our findings indicate that a station with a middle platform and two entrances positioned in the middle performed better in terms of dwell time in the case of alighting-dominant and mixed passenger flow. For stations experiencing boarding-dominant passenger flows, side platforms with multiple entrances at the ends and middle outperformed. Narrower platforms experienced significantly longer dwell times than other selected stations under similar demand. While the conclusion about the station design may not be generic, the proposed model provides a consistent and adaptable approach to study the impact of station design and passenger flows on urban rail dwell times, facilitating better-informed decision-making for station design or modification and enhancement of the overall rail system performance.