Connected and autonomous vehicles (CAVs) are on the way to the field application. In the beginning stage, there will be a mixed traffic flow, containing the regular human‐driven vehicles and CAVs with a low penetration rate. Recently, the discussion about the impact of a small proportion of CAVs in the mixed traffic is controversial. This paper investigated the possibility of applying the limited data from these lowly penetrated CAVs to estimate the average freeway link speeds based on the Kalman filtering (KF) method. First, this paper established a VISSIM‐based microsimulation model to mimic the mixed traffic with different CAV penetration rates. The characteristics of this mixed traffic were then discussed based on the simulation data, including the sample size distribution, data‐missing rate, speed difference, and fundamental diagram. Accordingly, the traditional KF‐based method was introduced and modified to adapt data from CAVs. Finally, the evaluations of the estimation accuracy and the sensitive analysis of the proposed method were conducted. The results revealed the possibility and applicability of link speed estimation using data from a small proportion of CAVs.