As small Unmanned Aerial Systems (UAS) proliferate, encounters between non-participants and UAS become much more frequent. Many of these are due to carelessness or not following rules on the part of the UAS operator. However, even when flying within the rules, encounters-potentially fatal-are possible. To help mitigate the risk of injury by UAS, health monitoring systems are imperative for reducing situations in which loss of control is likely. Current health monitoring tends to use real-time checks for power and navigation issues while a few systems are available for testing changes in vehicle responses to control inputs after flights. To reduce the likelihood of loss of control, we introduce a real-time health monitoring system that analyzes navigation, control, power, sensor, and communications integrity. Through experimental validation, we define metrics which detect degradations in the integrity of each system stated previously. Most failures present symptoms over time which can be detected, preventing the final catastrophic failure from occurring. Information requirements and necessary response times and thresholds are evaluated for each of the monitored subsystems, helping to define the implementation of each integrity check. Integration with a flight controller, particularly on small UAS which do not have the capacity to carry an auxiliary computer, is factored into the architecture, ensuring that health monitoring does not adversely affect flight control. Overall, this architecture provides a template and the considerations necessary for implementing more robust realtime health monitoring systems on the various UAS flight systems in operation.