Systems and methods are provided for isolating performance variation in website monitoring. A set of geographically diverse monitoring agents are identified and a subset of baseline agents is selected from these monitoring agents. The baseline agents are those agents that are geographically close to the target website or otherwise enjoy reliable communications with the target website and are therefore less affected by network latencies. The frequency at which a target website is monitored is weighted in favor of the baseline agents in order to get an accurate baseline metric for the target website while also obtaining information regarding global accessibility of the website from the geographically disperse monitoring agents. The variations in sample frequency can be optimized for each particular set of baseline agents. The set of baseline agents can be pre-assigned or dynamically identified based on an analysis of the performance variation from each of the monitoring agents.