When a citizen reports a crime, the first law enforcement respondent is normally a deputy from the Patrol Division. That deputy then conducts the original interviews and files the first crime report. Under usual circumstances, detectives are then assigned to perform subsequent investigations.

Investigators working out of the Encinitas Station are assigned as auto theft detectives and others have geographic "beats" in the three contract cities and the unincorporated areas of Rancho Santa Fe and Fairbanks Ranch. The Encinitas Station is unusual in San Diego County in that it acts as the police department for three cities and a large unincorporated area. Most Sheriff's stations serve only one city and the unincorporated areas contiguous to that city.

Encinitas Station detectives investigate cases involving theft, physical assaults (up to murder), sexual assaults, vandalism, burglaries, annoying phone calls and other crimes. Specialized investigative units such as Homicide, Bomb/Arson, Fraud, Domestic Violence, Computer Crime, Child Abuse and Narcotics handle those specific crimes for the entire Sheriff's jurisdiction, including the Encinitas command area.

School Resource Officers handle all crimes relating to school students at the middle and high school levels in Encinitas. These crimes include truancy, tobacco, drug and alcohol related offenses as well as crimes that occur on school grounds.