Traffic congestion is a major externality in modern transportation systems with negative economic, environmental and social impacts. Freeway bottlenecks are one of the key elements besides the demand for travel by automobiles that determine the extent of congestion. The primary objective of this research is to provide a better understanding of factors for variations in bottleneck discharge rates. Specifically this research seeks to (i) develop a methodology comparable to the rigorous methods to identify bottlenecks and measure capacity drop and its temporal (day to day) variations in a region, (ii) understand the variations in discharge rate of a freeway weaving bottleneck with a HOV lane and (iii) understand the relationship between lane flow distribution and discharge rate on a weaving bottleneck resulted from a lane drop and a busy off-ramp. In this research, a methodology has been developed to de-noise raw data using Discrete Wavelet Transforms (DWT). The de-noised data is then used to precisely identify bottleneck activation and deactivation times, and measure pre-congestion and congestion flows using Continuous Wavelet Transforms (CWT). To this end a methodology which could be used efficiently to identify and analyze freeway bottlenecks in a region in a consistent, reproducible manner was developed. Using this methodology, 23 bottlenecks have been identified in the Phoenix metropolitan region, some of which result in long queues and large delays during rush-hour periods. A study of variations in discharge rate of a freeway weaving bottleneck with a HOV lane showed that the bottleneck discharge rate diminished by 3-25% upon queue formations, however, the discharge rate recovered shortly thereafter upon high-occupancy-vehicle (HOV) lane activation and HOV lane flow distribution (LFD) has a significant effect on the bottleneck discharge rate: the higher the HOV LFD, the lower the bottleneck discharge rate. The effect of lane flow distribution and its relationship with bottleneck discharge rate on a weaving bottleneck formed by a lane drop and a busy off-ramp was studied. The results showed that the bottleneck discharge rate and lane flow distribution are linearly related and higher utilization of the median lane results in higher bottleneck discharge rate.