The efficient management of Cloud infrastructure and deployments is a topic that is currently attracting significant interest. Complex Cloud deployments can result in an intricate layered structure. Understanding the behaviour of these hierarchical systems and how to manage them optimally are challenging tasks that can be facilitated by pervasive monitoring. Monitoring tools and techniques have an important role to play in this area by gathering the information required to make informed decisions. A broad variety of monitoring tools are available, from general-purpose infrastructure monitoring tools that predate Cloud computing, to high-level application monitoring services that are themselves hosted in the Cloud. Surveying the capabilities of monitoring tools can identify the fitness of these tools in serving certain objectives. Monitoring tools are essential components to deal with various objectives of both Cloud providers and consumers in different Cloud operational areas. We have identified the practical capabilities that an ideal monitoring tool should possess to serve the objectives in these operational areas. Based on these identified capabilities, we present a taxonomy and analyse the monitoring tools to determine their strength and weaknesses. In conclusion, we present our reflections on the analysis, discuss challenges and identify future research trends in the area of Cloud monitoring.