An upward trend in cyber incidents across both U.K. and U.S. hospitals has been observed since 2015. Attacks range from identity theft to insurance fraud and extortion/blackmail. The Electronic Medical Record (EMR) systems used in hospitals are targeted due to the sensitivity of data within a healthcare setting. This work is motivated by the necessity to protect patient information and to ensure the availability of such EMR systems. A failure in either case can have grave implications for patients being treated and practitioners using the system. In this research, we propose the application of Machine Learning (ML) and Time Series (TS) anomaly detection to the problem of confidentiality and availability attacks on EMR systems. The results presented in this paper indicate that confidentiality incident detection is fully achievable using ML, with Support Vector Machines obtaining the highest accuracy, precision and recall of a number of models tested. Results from the availability prototype show that the detection of a message surge is possible within 10 seconds, by using an Exponential Moving Average implementation to identify anomalies in message flow. This finding paves the way for an automated surge defence to be developed, presenting a significant advance over the manual method used today. The feasibility and practicality of implementing these detection systems in a clinical setting are also discussed with consideration of parameter tuning, skill-sets, and data protection.